Factors associated with carriage of carbapenem-non-susceptible Enterobacteriaceaein North-Eastern France and outcomes of infected patients.

Background: Carbapenems are frequently used as a last resort to treat infections caused by multidrug-resistant Gram-negative organisms, thus carbapenem-non-susceptible Enterobacteriaceae (CNSE) is an emerging health threat. Objectives: To assess risk factors and outcomes of CNSE carriage. Patients and methods: We conducted a matched case-control study in six hospitals in North-Eastern France. The controls were patients harbouring carbapenem-susceptible Enterobacteriaceae. Fifty-five cases and 110 controls were included. Results: Most of the CNSE isolates were Enterobacter cloacae and Klebsiella pneumoniae . Carbapenemase production was observed in 40% of isolates and they produced OXA-48 only. CNSE carriage was significantly associated with recent antibiotic use ( P = 0.014), particularly carbapenems ( P = 0.03) and fluoroquinolones ( P = 0.016). A multivariate analysis using conditional logistic regression showed that the presence of concomitant infection(s) (OR: 9.83; 95% CI 3.04-21.39, P = 0.0031), nosocomial infections (OR: 7.84; 95% CI 2.00-12.54, P = 0.0063) and a high age (OR: 1.07; 95% CI 1.01-1.06, P = 0.038) were independently associated with CNSE carriage. Moreover, patients infected with CNSE had worse outcomes: fewer resolved infections at 1 month ( P = 0.02), and they had a higher mortality rate ( P = 0.0004) and longer hospital stays ( P = 0.02). Conclusions: We identified three independent risk factors for CNSE carriage as well as worse outcomes in infected patients in North-Eastern France. This highlights the importance of early detection of CNSE and the need for antimicrobial therapy re-evaluation after bacteriological analysis has been performed.

Extended spectrum ß-lactamase and plasmid mediated quinolone resistance in Escherichia coli fecal isolates from healthy companion animals in Algeria.

The aim of this study was to evaluate the rate of fecal carriage of Escherichia coli strains producing Extended-spectrum ß-lactamases (ESBLs) and plasmid-mediated quinolone resistance (PMQR) isolated from healthy pets (dogs and cats) in Algeria. Fecal samples from 171 healthy pets (102 dogs and 69 cats) in one veterinary practice and private owners were included. After isolates identification, antibiotic susceptibility was determined by disk diffusion procedure. ESBL were detected by combination disk tests. PCR and sequencing were used to characterize genes encoding ESBLs and PMQR. Transfer of ESBL and PMQR genes was assessed by conjugation experiments. Phylogenetic groups of E. coli were determined by PCR. Of the 171 animals, 20 carried an ESBL producing E. coli giving a prevalence of ESBL fecal carriage of 11.7%. All isolates were susceptible to carbapenems, cefoxitin, piperacillin-tazobactam, amikacin and fosfomycine. For the rest of the tested ß-lactams, susceptibility rates ranged from 35% to 70% for cefepime and amoxicillin-clavulanic acid respectively. Concerning the non-beta-lactams antibiotics, the rates of susceptibility ranged between 5% to trimethoprim and 95% for chloramphenicol. The beta-lactamase genes identified in E. coli isolates were blaCTX-M-15, blaCTX-M-1, blaSHV-12 and blaTEM-1. The PMQR determinants aac(6')-Ib-cr, qnrS1 and qnrB5 genes were identified in 15 isolates. Transconjugants were obtained for two isolates. Phylogenetic analysis showed that E. coli isolates belong to commensal phylogroups of A and B1. We reported here for the first time in Algeria ESBL and PMQR-producing E. coli in healthy cats and dogs.

Gardnerella vaginalis ventilatory acquired pneumonia among patients with trauma.

Gardnerella vaginalis (G. vaginalis) is a bacterium rarely responsible for systemic infections and is exceptionally isolated from bronchopulmonary samples. Here, we report here two patients with trauma who were diagnosed with a G. vaginalis ventilatory acquired pneumonia (VAP) via mini bronchoalveolar lavage (mini-BAL). According to our observations, G. vaginalis was the only microorganism with a significant threshold and the identification was obtained by a reliable mean. There is no recommendation for antibiotic treatment for invasive G. vaginalis infection. We treated these infections with Cefotaxim and Metronidazole which clinically improved the infection. To determine whether the two patients were infected by the same strain, we used a random amplified polymorphic DNA (RAPD) technique. The two G. vaginalis organisms had distinct RAPD profiles, suggesting the absence of cross-transmission. These two cases of trauma and G. vaginalis VAP suggest that this infection cannot be ruled out and should alert the clinician to treat it.

Genetic Diversity and Population Structure of Mycobacterium bovis at the Human-Animal-Ecosystem Interface in France: "A One Health Approach".

Mycobacterium bovis infects cattle and wildlife, and also causes a small proportion of tuberculosis cases in humans. In most European countries, M. bovis infections in cattle have been drastically reduced, but not eradicated. Here, to determine the M. bovis circulation within and between the human, cattle, and wildlife compartments, we characterized by spoligotyping and mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) typing the genetic diversity of M. bovis isolates collected from humans, cattle, and wildlife in France from 2000 to 2010. We also assessed their genetic structure within and among the different host groups, and across time and space. The M. bovis genetic structure and its spatiotemporal variations showed different dynamics in the human and animal compartments. Most genotypes detected in human isolates were absent in cattle and wildlife isolates, possibly because in patients, M. bovis infection was contracted abroad or was the reactivation of an old lesion. Therefore, they did not match the genetic pool present in France during the study period. However, some human-cattle exchanges occurred because some genotypes were common to both compartments. This study provides new elements for understanding M. bovis epidemiology in France, and calls for increased efforts to control this pathogen worldwide.

Description of a 2,683-base-pair plasmid containing qnrD in two Providencia rettgeri isolates.

qnr genes are plasmid-mediated quinolone resistance genes mainly harbored on large conjugative multiresistant plasmids. The qnrD gene was recently observed in Salmonella enterica on a small nonconjugative plasmid (p2007057). We describe two strains of Providencia rettgeri harboring qnrD on nonconjugative plasmids. The plasmids were 99% identical, with 2,683 bp and four open reading frames, including qnrD, but exhibited only 53% identity with the plasmid found in S. enterica.

Characterization of extended-spectrum beta-lactamase-producing Salmonella enterica serotype Brunei and Heidelberg at the Hussein Dey hospital in Algiers (Algeria).

The purpose of this work was to study the genetic determinants responsible for extended-spectrum cephalosporin (ESC) resistance of Salmonella collected during the period of 1995-2008 at the Hussein Dey hospital in Algiers (Algeria). Fourteen ESC-resistant Salmonella isolates were tested towards 22 antimicrobial agents. Polymerase chain reaction (PCR) and sequencing were used to determine the underlying genetic determinants responsible for the extended-spectrum beta-lactamase (ESBL) phenotypes. Enterobacterial Repetitive Intergenic Consensus PCR was employed to type the isolates. All tested isolates were resistant to ticarcillin, ticarcillin-clavulanate, piperacillin, cefuroxime, aztreonam, ceftazidime, cefotaxime (except two isolates), cefepime, and cefpirome. PCR and DNA sequencing identified these ESBLs as TEM-48 (n=6), TEM-4 (n=3), CTX-M-15 (n=4), and one new TEM, designated TEM-188. Thus, continued surveillance for the presence of ESBL-producing (non-typhoidal) salmonellae in Algeria is essential.

Rapid detection of aac(6')-Ib-cr quinolone resistance gene by pyrosequencing.

Pyrosequencing was used to rapidly detect aac(6')-Ib and aac(6')-Ib-cr genes. This plasmid-mediated quinolone resistance determinant is increasing in extended-spectrum beta-lactamase-producing Enterobacteriaceae. This method is faster and more cost-effective than the methods previously described. Sequences obtained with this pyrosequencing method showed 100% concordance with conventional sequencing.

First description of IncX3 NDM-5-producing plasmid within Escherichia coli ST448 in Mali.

Carbapenem resistance in Enterobacteriaceae has become an increasingly worrying threat. So far, no epidemiological data regarding NDM-producing enterobacterial isolates has been available on these strains in West Africa. The aim of this study was to seek for carbapenemase-producing Enterobacteriaceae clinical strains isolated in Bamako Teaching Hospital in Mali. Of 50 strains isolated between May 2016 and September 2016, we found a ST448 E. coli harbouring an IncX3 plasmid with bla NDM-5 embedded in the ΔISAba125-ble MBL structure. This study reports the first description of NDM-5 in Mali isolated in an undescribed ST E. coli in West Africa.

Cutibacterium acnes Biofilm Study during Bone Cells Interaction.

Cutibacterium acnes is an opportunistic pathogen involved in Bone and Prosthesis Infections (BPIs). In this study, we observed the behavior of commensal and BPI C. acnes strains in the bone environment through bacterial internalization by osteoblast-like cells and biofilm formation. For the commensal strains, less than 1% of the bacteria were internalized; among them, about 32.7 ± 3.9% persisted intracellularly for up to 48 h. C. acnes infection seems to have no cytotoxic effect on bone cells as detected by LDH assay. Interestingly, commensal C. acnes showed a significant increase in biofilm formation after osteoblast-like internalization for 50% of the strains (2.8-fold increase). This phenomenon is exacerbated on a titanium support, a material used for medical devices. For the BPI clinical strains, we did not notice any increase in biofilm formation after internalization despite a similar internalization rate by the osteoblast-like cells. Furthermore, fluorescent staining revealed more live bacteria within the biofilm after osteoblast-like cell interaction, for all strains (BPIs and commensal). The genomic study did not reveal any link between their clinical origin and phylotype. In conclusion, we have shown for the first time the possible influence of internalization by osteoblast-like cells on commensal C. acnes.

Characterization of Carbapenem-Resistant Enterobacteriaceae Clinical Isolates in Al Thawra University Hospital, Sana'a, Yemen.

Objective: The aim of this study was to investigate the resistance mechanisms of carbapenem-resistant Enterobacteriaceae clinical strains recovered from Al Thawra University Hospital, Sana'a, Yemen. Methods: A total of 27 isolates showing decreased susceptibility to carbapenems were obtained from different clinical specimens in Al Thawra Hospital, Sana'a, Yemen. Strains were identified by Matrix Assisted Laser Desorption Ionization Time-Of-Flight spectroscopy. Susceptibility to antibiotics was determined by the disk diffusion method on Mueller Hinton agar. Carbapenemases-encoding genes, extended-spectrum ß-lactamases (ESBLs), and plasmid-mediated quinolone resistance (PMQR) genes were screened by PCR. Bacterial isolates were typed by multilocus sequence typing (MLST). Results: Carbapenemase genes detection and sequencing showed that 18 (66.7%) isolates were Klebsiella pneumoniae (NDM-1, n = 13; NDM-1 + OXA-48, n = 3; OXA-48, n = 1; OXA-232, n = 1), 6 (22.2%) were Escherichia coli (NDM-5, n = 3; OXA-181, n = 2; OXA-48, n = 1), and 3 (11.1%) were Enterobacter cloacae (NDM-1, n = 1; OXA-181, n = 2). In addition the ESBL gene blaCTX-M-15 was detected in 14 K. pneumoniae and 2 E. coli isolates, and the blaCTX-M-216 was found in 1 E. coli isolate. Fifteen isolates were PMQR positive including qnrB1 (n = 1), qnrS1 (n = 5), qnrS4 (n = 2), and aac-(6')-Ib-cr (n = 7). The MLST typing showed a diversity of sequence type (ST) clones including Escherichia coli ST410 (3), ST448 (2), and ST648; Enterobacter cloacae ST78 and ST270; and Klebsiella pneumoniae ST395 (2), ST309, ST23, ST35, ST1728, ST15, ST231, and ST1428. Conclusion: This study reports the first description of OXA-48-like-producing Enterobacteriaceae and NDM-5 enzymes in E. coli in Yemen.

Occurrence of Carbapenemase-Producing Klebsiella pneumoniae in Bat Guano.

The aim of this study was to screen for the presence of carbapenemase-producing Enterobacteriaceae (CPE) isolates from bat guano in Bejaia, Algeria. Guano samples (n = 110) were collected in Aokas's cave, Bejaia, Algeria, between March and May 2016. Samples were plated on MacConkey agar supplemented with ertapenem (0.5 mg/L) and vancomycin (32 mg/L). The isolates were identified and antimicrobial susceptibility was determined using disk diffusion method. Carbapenemase, extended spectrum ß-lactamases, plasmid-mediated AmpC, and plasmid-mediated quinolone resistance genes were studied using PCR and sequencing. Clonal relatedness was studied using multilocus sequence typing (MLST). Two CPE isolates were identified as Klebsiella pneumoniae. PCR and sequencing identified the blaOXA-48 in one K. pneumoniae strain (CS34) and blaKPC-3 in the other strain (CS63). K. pneumoniae CS63 was found to carry blaTEM-1 and aac(6')-Ib genes. The MLST showed that K. pneumoniae CS63 was assigned to ST512, whereas K. pneumoniae CS34 belonged to ST1878. This is the first description of CPE from bats' guano.

Difficult Gram staining: a case of endocarditis due to Cardiobacterium hominis and review of the literature.

Cardiobacterium hominis est un bacille à Gram négatif responsable d'endocardites infectieuses, principalement chez les patients atteints de pathologies cardiaques ou porteurs de valves. L'identification de cette bactérie est souvent complexe et peut être la cause d'un diagnostic et d'une prise en charge tardifs, source de complications cardiaques. Cet article présente la prise en charge d'une endocardite infectieuse associée à un sepsis à Cardiobacterium hominis, les difficultés d'identification de cette bactérie, ainsi qu'une revue de la littérature sur les infections dues à cette bactérie.

First report of qnrB-producing Enterobacter cloacae and qnrA-producing Acinetobacter baumannii recovered from Algerian hospitals.

Two isolates of Enterobacter cloacae and 1 isolate of Acinetobacter baumannii showing a multidrug resistance phenotype including resistance to beta-lactams and fluoroquinolones were included in this study. By polymerase chain reaction amplification and sequencing, the 2 isolates of E. cloacae were found to produce QnrB and the A. baumannii isolate was found to produce QnrA. In addition, the 2 E. cloacae isolates were found to produce CTX-M-15.

Clonal dissemination of OXA-48-producing Enterobacter cloacae isolates from companion animals in Algeria.

OBJECTIVES: The aim of this study was to investigate carbapenemase-producing Enterobacteriaceae (CPE) in companion animals. METHODS: Between October 2015 and April 2016, 533 rectal swabs were obtained from healthy and diseased pets in different cities in Algeria. Samples were plated on MacConkey agar supplemented with ertapenem (0.5mg/L). Isolates were identified by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF/MS). Antimicrobial susceptibility testing was performed by the disk diffusion method. Carbapenemase, plasmid-mediated AmpC (pAmpC), extended-spectrum ß-lactamase (ESBL) and plasmid-mediated quinolone resistance genes were characterised by PCR. Plasmids were extracted by the Kieser extraction method and were analysed by PCR-based replicon typing (PBRT). The epidemiological relationship between Enterobacter cloacae isolates was determined by random amplified polymorphic DNA (RAPD) analysis and multilocus sequence typing (MLST). RESULTS: From 533 rectal swabs, 12 Enterobacteriaceae (2.3%), including 2 Escherichia coli, 2 Klebsiella pneumoniae and 8 E. cloacae, were recovered from selection plates. The 12 strains were resistant to amoxicillin/clavulanic acid, ticarcillin, piperacillin/tazobactam and ertapenem. All isolates were susceptible to aminoglycosides, imipenem and extended-spectrum cephalosporins. PCR and sequencing identified the blaOXA-48 gene in all isolates. qnrB1 was identified in all E. cloacae isolates. Plasmid analysis showed that the blaOXA-48 gene was localised on a 7-kb untypeable plasmid. RAPD analysis demonstrated the presence of the same profile pattern in the eight E. cloacae isolates. MLST analysis showed that the E. cloacae isolates belonged to ST527. CONCLUSIONS: This study reports for the first time the presence of CPE in horses and pet birds in the world.

Prevalence of a New Variant OXA-204 and OXA-48 Carbapenemases Plasmids Encoded in Klebsiella pneumoniae Clinical Isolates in Tunisia.

Carbapenemase-producing Klebsiella pneumoniae strains have emerged as a major problem for healthcare systems. The aim of this study was to determine the role and diversity of plasmids harboring carbapenemases encoding genes from a collection of K. pneumoniae isolates recovered between July 2011 and January 2012, with decreased susceptibility to carbapenems. Imipenem (IPM), ertapenem (ETP), meropenem (MEM), and doripenem (DOR) minimum inhibitory concentrations (MICs) were determined by E-test. Carbapenemase production was detected with the modified Hodge test. ß-Lactamases encoding genes were amplified by PCR and sequenced. Plasmid incompatibility groups harbored by carbapenemases producers were investigated using the PCR-based replicon typing method and the clonal relationship of the isolates was investigated by pulse filed electrophoresis. IMP, ertapenem, meropenem, and doripenem MICs ranged between 0.25 and 16 mg/L. Carbapenemase activity was detected in 14 isolates. Two carbapenemases were identified: OXA-48 in 13 isolates and a new variant OXA-204 in 1 isolate, in combination with extended-spectrum ß-lactamases, CTX-M-1, CTX-M-9, CTX-M-14, CTX-M-15, and VEB-8. One isolate produced CMY-2. OXA-48 and the new variant OXA-204 were confirmed as transferable plasmid encoded. The carbapenemase-producing K. pneumoniae harbored plasmids of the A/C, LVPK, and L/M replicon types. Thirteen different pulso types were observed. Three pairs of isolates showed a clonal relatedness. This diversity in ß-lactamases, in pulso types and in plasmid content, shows the ability of OXA-type carbapenemase to disseminate. This is worrying for the control of the increase in antibiotic resistance frequency and necessitates that continuous investigations in the clinical setting remain a high priority to clarify the contribution of antimicrobial use into multiresistance bacterial dissemination.

Characterization of CTX-M-15-producing Klebsiella pneumoniae and Escherichia coli strains isolated from hospital environments in Algeria.

For detecting extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae in the hospital environment, sedimentation plates were placed in the rooms of two hospitals. Three environmental isolates, two Klebsiella pneumoniae, and one Escherichia coli resistant to extended-spectrum cephalosporins with a phenotype indicating CTX-M enzymes production (the minimum inhibitory concentration [MIC] of cefotaxime was higher than the MIC of ceftazidime) were recovered. By PCR and sequencing, the three isolates were found to produce CTX-M-15. The bla(CTX-M-15) genes in the three isolates were transferred by conjugation. One K. pneumoniae environmental isolate showed an identical and unique RAPD profile with two other K. pneumoniae clinical isolates recovered from urinary tract infection from patients hospitalized in two different wards of another hospital.

Nocardiose cutanée chez une patiente immunocompétente A propos d'un cas et revue de la littérature.

Nocardia spp. est responsable d'infections opportunistes chez les patients immunodéprimés, principalement d'infections pulmonaires. Le système nerveux central est la localisation extra-pulmonaire la plus souvent retrouvée. Nous rapportons ici un cas d'infection cutanée à N. brasiliensis chez une patiente immunocompétente, ainsi qu'une revue de la littérature.

Fecal Carriage of Extended-Spectrum ß-Lactamase-Producing Enterobacteriaceae Strains Is Associated with Worse Outcome in Patients Hospitalized in the Pediatric Oncology Unit of Beni-Messous Hospital in Algiers, Algeria.

OBJECTIVES: The current study aimed to investigate extended-spectrum ß-lactamase-producing Enterobacteriaceae (ESBL-E) fecal carriage in children with different cancers admitted in the pediatric oncology unit of Beni-Messous Hospital (Algiers, Algeria). MATERIALS AND METHODS: Rectal swabs from children with cancer were sampled from February 2012 to May 2013 within 48 hours following their admission. After species identification and detection of ESBL production by double-disk synergy test (DD test), antibiotic susceptibility was determined by the standard disk diffusion method. Antibiotic resistance genes, including bla genes and plasmid-mediated quinolone resistance (PMQR) genes, were investigated by polymerase chain reaction (PCR). The phylogenetic grouping of Escherichia coli strains was determined by PCR. RESULTS: Of the 171 children studied, 93 (54%) were ESBL carriers. An antibiotic treatment for the last 3 months before admission (p = 0.01), hematological malignancies (p = 0.003), and death (p = 0.0003) were more frequent in the ESBL-E group than in the non-ESBL group. Multivariate analysis showed that hematological malignancies (odds ratio [OR]: 3.9; confidence interval [CI]: 1.1-14.1; p = 0.04) and ESBL-E carriage (OR: 6.2; CI: 1.7-22.00; p = 0.005) were two independent factors associated with increased risk of death. A total of 103 ESBL-E isolates were obtained. Klebsiella pneumoniae and E. coli isolates were the most frequently isolated. PCR amplification showed that all the isolates produced a CTX-M ESBL (CTX-M-15, CTX-M-14, and CTX-M-3). The PMQR genes detected were qnrB, qnrS, and aac(6')-Ib-cr. E. coli isolates were assigned to four major extraintestinal pathogenic E. coli phylogroups, including B2 and D. CONCLUSION: This study provides, for the first time, insight into epidemiology of the ESBL-E fecal carriage among children with cancer in Algeria.

First report of CTX-M-15 and CTX-M-3 beta-lactamases among clinical isolates of Enterobacteriaceae in Béjaia, Algeria.

We assessed the prevalence and phenotypic characteristics of extended-spectrum beta-lactamase producers among 365 clinical isolates of members of the family Enterobacteriaceae recovered from two hospitals in Béjaia, Algeria, between March 2004 and April 2005. Twenty-one strains were resistant to cefotaxime and/or ceftazidime. A double-disk synergy test yielded a positive result in five cases (three Escherichia coli, one Klebsiella pneumoniae and one Enterobacter cloacae). Using polymerase chain reaction and sequencing, the three E. coli isolates and the K. pneumoniae isolate were found to produce extended-spectrum beta-lactamase CTX-M-15 and the E. cloacae isolate produced CTX-M-3. The three CTX-M-15-producing E. coli isolates were not isolated in the same wards, although genotyping by randomly amplified polymorphic DNA analysis revealed that they were clonally related. The bla(CTX-M-15) genes were transferred from E. coli by conjugation, whilst conjugative transfer of bla(CTX-M) genes from K. pneumoniae and E. cloacae was not detectable.

Emergence of Carbapenemase-Producing Escherichia coli Isolated from Companion Animals in Algeria.

The emergence and worldwide spread of carbapenemase-producing Enterobacteriaceae is of great concern to public health. The aim of this study was to investigate the occurrence of carbapenemase-producing Escherichia coli in companion animals in Algeria. Two hundred fecal samples were obtained from healthy and diseased dogs and cats in one veterinary office and private owners in Bejaia city, Algeria, during November 2014 to March 2015. Isolates were screened by polymerase chain reaction for the presence of carbapenemase, acquired plasmidic AmpC (pAmpC) and extended-spectrum beta-lactamase genes. Five carbapenemase-producing E. coli isolates were detected including four OXA-48-producing isolates and one isolate producing NDM-5. Coexpression of ESBL and pAmpC genes was observed in these isolates. Phylogenetic grouping revealed that these isolates belonged to A and D phylogroups. The results of this study show that carbapenemase-producing E. coli spread to the companion animals in Algeria.